OMOPHub MCP Server

An MCP server that puts the OHDSI OMOP standardized vocabularies — SNOMED CT, ICD-10, RxNorm, LOINC and 100+ others — behind Claude as searchable, mappable concepts, instead of requiring a multi-gigabyte ATHENA download and a local database.

   
Type MCP server
Supplier OMOPHub (open source, MIT)
Availability GA — npm @omophub/omophub-mcp 1.5.3; repo last pushed 2026-07-28
Pricing Free / OSS (MIT) for the server. The backing API at api.omophub.com requires a free account and an API key; Unverified — the README documents an upgrade path for higher rate limits at dashboard.omophub.com/billing but does not state the free-tier limits or paid prices.
Capabilities Read-only — vocabulary search, concept lookup, mapping and hierarchy traversal
Verified degraded · 2026-08-06 — auth-gated (requires an OMOPHUB_API_KEY signup), so functionally unverifiable without an account; launch command confirmed current
Security cleared · 2026-08-06 — provenance matches OMOPHub/omophub-mcp, MIT, no advisories

How to install

You need an API key first: sign up at omophub.com, then create a key at dashboard.omophub.com/api-keys. Keys are prefixed oh_. Node.js 20 or newer is required (engines.node: >=20 in the published package).

  • Claude Code — stdio via npx, with the key passed as an environment variable: 
    claude mcp add omophub --env OMOPHUB_API_KEY=oh_your_key_here -- npx -y @omophub/omophub-mcp

    (The upstream README shows claude mcp add omophub -- npx -y @omophub/omophub-mcp without the key; the server will not authenticate unless OMOPHUB_API_KEY is set, so use the --env form above.)

  • Claude Desktop — add to claude_desktop_config.json: 
    {
  "mcpServers": {
    "omophub": {
      "command": "npx",
      "args": ["-y", "@omophub/omophub-mcp"],
      "env": {
        "OMOPHUB_API_KEY": "oh_your_key_here"
      }
    }
  }
}
  • Docker (optional, HTTP on port 3100 — a long-lived service you keep running, not a one-shot): 
    docker run -e OMOPHUB_API_KEY=oh_your_key_here -p 3100:3100 omophub/omophub-mcp

    then register it with claude mcp add --transport http omophub http://localhost:3100/mcp.

  • Claude Code — HTTP without Docker, same long-lived-service caveat: 
    npx -y @omophub/omophub-mcp --transport=http --port=3100 --api-key=oh_your_key_here

What it does

Eleven tools over the OMOP vocabulary tables:

  • Search and lookup — search_concepts, get_concept, get_concept_by_code, semantic_search, find_similar_concepts.
  • Mapping and navigation — map_concept (cross-vocabulary mapping, e.g. ICD-10 → SNOMED CT standard concept), get_hierarchy (ancestor/descendant traversal), explore_concept.
  • FHIR — fhir_resolve and fhir_resolve_codeable_concept, for turning FHIR codings into OMOP standard concepts.
  • Reference — list_vocabularies, plus resources omophub://vocabularies and omophub://vocabularies/{vocabulary_id}.
  • Guided prompts — phenotype-concept-set (build a concept set for a phenotype definition) and code-lookup.

Primary use cases: building OMOP concept sets for cohort/phenotype definitions, mapping source codes to standard concepts during ETL, resolving FHIR codings to OMOP.

Notes

This is a vocabulary service, not a database query server — it answers “what concept is this code, and what does it map to”, not “how many patients in my CDM have it”. For querying an actual OMOP CDM instance from Claude, see pyomop. For a non-OMOP terminology server covering ICD-11, SNOMED CT, LOINC, RxNorm, MeSH and ATC, see Medical Terminologies MCP.

A hosted endpoint exists at https://mcp.omophub.com but expects the key as a Bearer token in an Authorization header. The README notes that Claude Desktop’s Custom Connectors UI only supports OAuth and cannot send custom headers, so the npx stdio path above is the recommended route for Desktop.

Vocabulary content itself carries the licenses of its sources — SNOMED CT in particular requires an affiliate license in non-member countries, and the OMOP wrapper does not change that.

Sources

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